How to bake floating geometry to normal map?
So here is what’s happening. Let say you have object A (the highpoly object you need to bake) and object B (the lowpoly, the object on which you want to use the bake)


The bake is a kind of scan that begins from the faces and goes in the opposite direction of their normals, it goes as long as necessary, until it hits the surface of the object that needs to be baked. That’s the basis of baking (as I understand it). So here is what happens for the top face: With a Ray Distance of 0 the scan begins from the top face, it goes downwards and hit nothing, so no baking.





If some faces of object A go a bit beyond the surface of object B, you need to make the scan begin a bit before with the help of the Ray Distance value. It’s the case here, object A is out of object B, so you need to have a Ray Distance value higher than 0, in your file your value was a bit low, so it didn’t scan the whole object A, you need to increase the value a bit, 0.2 seems good.





The bottom face of your object B scanned in the opposite direction of its normal as it is supposed to do, so it scanned upwards until it hit object A. But in this direction it hits faces that are flipped, so the scan gave incorrect colors.





I suppose you didn't expect the bottom face to have any baking. In that case the simplest solutions are either to paint your normal map with purple, or to close the bottom of your object A with a face so that the object won't be scanned by the object B bottom face (only slopes can be scanned, not surfaces that are parallel or perpendicular to the scan direction).